MultiQC Report

Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Export Plots

Images
Data

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in multiqc_data when this report was generated.

Choose Plots

If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

Save Settings

You can save the toolbox settings for this report to the browser.

Load Settings

Choose a saved report profile from the dropdown box below:

Tool Citations

Please remember to cite the tools that you use in your analysis.

To help with this, you can download publication details of the tools mentioned in this report:

About MultiQC

This report was generated using MultiQC, version 1.21

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by:

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2024-04-11, 13:07 EDT based on data in: /work/gmgi/Fisheries/epiage/haddock/methylation/meth_extracted

General Statistics

Showing ⁶⁸/₆₈ rows and ⁴/₄ columns.

Sample Name	% mCpG	% mCHG	% mCHH	M C's
Mae-263_S1_R1_001_val_1	63.8%	1.6%	11.4%	1274.3
Mae-266_S2_R1_001_val_1	64.6%	1.8%	13.1%	1254.6
Mae-274_S3_R1_001_val_1	64.6%	1.1%	11.4%	1031.6
Mae-278_S4_R1_001_val_1	65.5%	1.2%	11.3%	1028.5
Mae-281_S5_R1_001_val_1	63.1%	1.2%	13.9%	1245.9
Mae-285_S6_R1_001_val_1	61.2%	1.7%	24.7%	651.8
Mae-293_S7_R1_001_val_1	63.7%	1.2%	10.0%	1159.0
Mae-294_S8_R1_001_val_1	66.4%	1.2%	10.7%	1408.5
Mae-295_S9_R1_001_val_1	64.6%	1.2%	11.0%	844.0
Mae-298_S10_R1_001_val_1	64.0%	1.4%	13.2%	1115.1
Mae-302_S11_R1_001_val_1	63.9%	1.3%	14.1%	690.5
Mae-305_S12_R1_001_val_1	63.4%	1.2%	17.3%	945.6
Mae-310_S13_R1_001_val_1	63.6%	1.3%	12.4%	1166.6
Mae-311_S14_R1_001_val_1	63.8%	1.2%	10.0%	1405.8
Mae-317_S15_R1_001_val_1	65.3%	1.2%	9.3%	1021.1
Mae-322_S16_R1_001_val_1	64.6%	1.2%	11.2%	1437.5
Mae-327_S17_R1_001_val_1	64.4%	1.1%	10.6%	717.8
Mae-329_S18_R1_001_val_1	64.2%	1.1%	10.0%	1072.5
Mae-330_S19_R1_001_val_1	64.2%	1.2%	12.8%	1544.6
Mae-338_S20_R1_001_val_1	65.0%	1.4%	9.5%	1423.7
Mae-342_S21_R1_001_val_1	63.0%	1.2%	9.7%	1565.1
Mae-343_S22_R1_001_val_1	64.0%	1.3%	11.7%	1642.0
Mae-344_S23_R1_001_val_1	63.9%	1.4%	14.6%	1480.9
Mae-350_S24_R1_001_val_1	65.4%	1.4%	23.0%	1110.0
Mae-352_S25_R1_001_val_1	62.8%	1.4%	14.0%	916.3
Mae-356_S26_R1_001_val_1	63.7%	1.3%	12.0%	1059.6
Mae-368_S27_R1_001_val_1	65.6%	1.2%	10.3%	992.2
Mae-371_S28_R1_001_val_1	62.8%	1.1%	9.7%	893.4
Mae-378_S29_R1_001_val_1	63.3%	1.3%	10.1%	707.5
Mae-390_S32_R1_001_val_1	64.9%	1.2%	12.8%	1481.3
Mae-396_S33_R1_001_val_1	66.2%	1.3%	9.8%	895.0
Mae-399_S34_R1_001_val_1	65.7%	1.3%	9.6%	992.6
Mae-403_S35_R1_001_val_1	65.5%	1.4%	9.3%	829.2
Mae-405_S36_R1_001_val_1	64.6%	1.1%	8.8%	728.7
Mae-410_S37_R1_001_val_1	64.8%	1.4%	11.0%	702.1
Mae-414_S38_R1_001_val_1	64.3%	1.4%	12.3%	726.6
Mae-421_S39_R1_001_val_1	64.9%	1.3%	14.6%	835.0
Mae-422_S40_R1_001_val_1	63.7%	1.8%	13.5%	600.0
Mae-424_S41_R1_001_val_1	61.8%	1.6%	20.5%	574.0
Mae-428_S42_R1_001_val_1	63.5%	1.3%	12.3%	881.3
Mae-432_S43_R1_001_val_1	66.1%	1.3%	11.1%	987.9
Mae-436_S44_R1_001_val_1	65.5%	1.4%	9.3%	1141.8
Mae-440_S45_R1_001_val_1	64.4%	1.5%	12.1%	917.2
Mae-441_S46_R1_001_val_1	64.3%	1.3%	13.6%	926.0
Mae-449_S48_R1_001_val_1	64.5%	1.4%	11.0%	1490.3
Mae-454_S49_R1_001_val_1	65.6%	1.3%	9.3%	745.4
Mae-464_S50_R1_001_val_1	64.8%	1.3%	12.0%	609.3
Mae-468_S51_R1_001_val_1	63.8%	1.4%	12.1%	1148.4
Mae-470_S52_R1_001_val_1	63.6%	1.4%	11.2%	785.7
Mae-474_S57_R1_001_val_1	65.2%	1.3%	12.8%	1315.9
Mae-475_S53_R1_001_val_1	65.1%	1.2%	9.7%	1063.2
Mae-477_S54_R1_001_val_1	67.2%	1.3%	13.3%	1133.9
Mae-481_S55_R1_001_val_1	63.6%	1.3%	12.0%	1471.5
Mae-488_S56_R1_001_val_1	63.7%	1.1%	9.1%	1156.0
Mae-495_S47_R1_001_val_1	63.6%	1.3%	11.2%	799.3
Mae-496_S58_R1_001_val_1	64.1%	1.3%	9.6%	1005.8
Mae-499_S59_R1_001_val_1	68.1%	1.1%	12.8%	1337.5
Mae-501_S60_R1_001_val_1	66.1%	1.2%	10.6%	1439.3
Mae-502_S61_R1_001_val_1	66.5%	1.1%	11.0%	1183.7
Mae-509_S62_R1_001_val_1	64.7%	1.3%	9.4%	1543.3
Mae-512_S63_R1_001_val_1	64.1%	1.4%	10.6%	1506.7
Mae-519_S64_R1_001_val_1	63.8%	1.2%	14.4%	1034.8
Mae-520_S65_R1_001_val_1	65.1%	1.3%	12.9%	1032.3
Mae-524_S66_R1_001_val_1	64.6%	1.1%	9.7%	1174.0
Mae-525_S67_R1_001_val_1	66.1%	1.3%	9.4%	1536.9
Mae-533_S68_R1_001_val_1	65.3%	1.2%	11.5%	1649.9
Mae-535_S69_R1_001_val_1	64.1%	1.2%	12.7%	1587.4
Mae-537_S70_R1_001_val_1	61.3%	1.4%	10.9%	1815.4

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-general_stats_table

Sort	Group	Column	Description	ID	Scale
\|\|	Bismark	% mCpG	% Cytosines methylated in CpG context	`percent_cpg_meth`	None
\|\|	Bismark	% mCHG	% Cytosines methylated in CHG context	`percent_chg_meth`	None
\|\|	Bismark	% mCHH	% Cytosines methylated in CHH context	`percent_chh_meth`	None
\|\|	Bismark	M C's	Total number of C's analysed, in millions	`total_c`	None

Bismark

Version: 0.24.2

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.DOI: 10.1093/bioinformatics/btr167.

Cytosine Methylation

Created with MultiQC

Showing ⁶⁸/₆₈ rows and ³/₃ columns.

Sample Name	Methylated CpG	Methylated CHG	Methylated CHH
Mae-263_S1_R1_001_val_1	63.8%	1.6%	11.4%
Mae-266_S2_R1_001_val_1	64.6%	1.8%	13.1%
Mae-274_S3_R1_001_val_1	64.6%	1.1%	11.4%
Mae-278_S4_R1_001_val_1	65.5%	1.2%	11.3%
Mae-281_S5_R1_001_val_1	63.1%	1.2%	13.9%
Mae-285_S6_R1_001_val_1	61.2%	1.7%	24.7%
Mae-293_S7_R1_001_val_1	63.7%	1.2%	10.0%
Mae-294_S8_R1_001_val_1	66.4%	1.2%	10.7%
Mae-295_S9_R1_001_val_1	64.6%	1.2%	11.0%
Mae-298_S10_R1_001_val_1	64.0%	1.4%	13.2%
Mae-302_S11_R1_001_val_1	63.9%	1.3%	14.1%
Mae-305_S12_R1_001_val_1	63.4%	1.2%	17.3%
Mae-310_S13_R1_001_val_1	63.6%	1.3%	12.4%
Mae-311_S14_R1_001_val_1	63.8%	1.2%	10.0%
Mae-317_S15_R1_001_val_1	65.3%	1.2%	9.3%
Mae-322_S16_R1_001_val_1	64.6%	1.2%	11.2%
Mae-327_S17_R1_001_val_1	64.4%	1.1%	10.6%
Mae-329_S18_R1_001_val_1	64.2%	1.1%	10.0%
Mae-330_S19_R1_001_val_1	64.2%	1.2%	12.8%
Mae-338_S20_R1_001_val_1	65.0%	1.4%	9.5%
Mae-342_S21_R1_001_val_1	63.0%	1.2%	9.7%
Mae-343_S22_R1_001_val_1	64.0%	1.3%	11.7%
Mae-344_S23_R1_001_val_1	63.9%	1.4%	14.6%
Mae-350_S24_R1_001_val_1	65.4%	1.4%	23.0%
Mae-352_S25_R1_001_val_1	62.8%	1.4%	14.0%
Mae-356_S26_R1_001_val_1	63.7%	1.3%	12.0%
Mae-368_S27_R1_001_val_1	65.6%	1.2%	10.3%
Mae-371_S28_R1_001_val_1	62.8%	1.1%	9.7%
Mae-378_S29_R1_001_val_1	63.3%	1.3%	10.1%
Mae-390_S32_R1_001_val_1	64.9%	1.2%	12.8%
Mae-396_S33_R1_001_val_1	66.2%	1.3%	9.8%
Mae-399_S34_R1_001_val_1	65.7%	1.3%	9.6%
Mae-403_S35_R1_001_val_1	65.5%	1.4%	9.3%
Mae-405_S36_R1_001_val_1	64.6%	1.1%	8.8%
Mae-410_S37_R1_001_val_1	64.8%	1.4%	11.0%
Mae-414_S38_R1_001_val_1	64.3%	1.4%	12.3%
Mae-421_S39_R1_001_val_1	64.9%	1.3%	14.6%
Mae-422_S40_R1_001_val_1	63.7%	1.8%	13.5%
Mae-424_S41_R1_001_val_1	61.8%	1.6%	20.5%
Mae-428_S42_R1_001_val_1	63.5%	1.3%	12.3%
Mae-432_S43_R1_001_val_1	66.1%	1.3%	11.1%
Mae-436_S44_R1_001_val_1	65.5%	1.4%	9.3%
Mae-440_S45_R1_001_val_1	64.4%	1.5%	12.1%
Mae-441_S46_R1_001_val_1	64.3%	1.3%	13.6%
Mae-449_S48_R1_001_val_1	64.5%	1.4%	11.0%
Mae-454_S49_R1_001_val_1	65.6%	1.3%	9.3%
Mae-464_S50_R1_001_val_1	64.8%	1.3%	12.0%
Mae-468_S51_R1_001_val_1	63.8%	1.4%	12.1%
Mae-470_S52_R1_001_val_1	63.6%	1.4%	11.2%
Mae-474_S57_R1_001_val_1	65.2%	1.3%	12.8%
Mae-475_S53_R1_001_val_1	65.1%	1.2%	9.7%
Mae-477_S54_R1_001_val_1	67.2%	1.3%	13.3%
Mae-481_S55_R1_001_val_1	63.6%	1.3%	12.0%
Mae-488_S56_R1_001_val_1	63.7%	1.1%	9.1%
Mae-495_S47_R1_001_val_1	63.6%	1.3%	11.2%
Mae-496_S58_R1_001_val_1	64.1%	1.3%	9.6%
Mae-499_S59_R1_001_val_1	68.1%	1.1%	12.8%
Mae-501_S60_R1_001_val_1	66.1%	1.2%	10.6%
Mae-502_S61_R1_001_val_1	66.5%	1.1%	11.0%
Mae-509_S62_R1_001_val_1	64.7%	1.3%	9.4%
Mae-512_S63_R1_001_val_1	64.1%	1.4%	10.6%
Mae-519_S64_R1_001_val_1	63.8%	1.2%	14.4%
Mae-520_S65_R1_001_val_1	65.1%	1.3%	12.9%
Mae-524_S66_R1_001_val_1	64.6%	1.1%	9.7%
Mae-525_S67_R1_001_val_1	66.1%	1.3%	9.4%
Mae-533_S68_R1_001_val_1	65.3%	1.2%	11.5%
Mae-535_S69_R1_001_val_1	64.1%	1.2%	12.7%
Mae-537_S70_R1_001_val_1	61.3%	1.4%	10.9%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: table-bismark-methylation-dp

Sort	Column	Description	ID	Scale
\|\|	Methylated CpG	Methylated CpG	`percent_cpg_meth`	None
\|\|	Methylated CHG	Methylated CHG	`percent_chg_meth`	None
\|\|	Methylated CHH	Methylated CHH	`percent_chh_meth`	None

M-Bias

This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
Bismark	`0.24.2`

Toggle navigation v1.21

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

General Statistics

General Statistics: Columns

Bismark

Cytosine Methylation

Table-Bismark-Methylation-Dp: Columns

M-Bias

Software Versions

v1.21

Highlight Samples

Rename Samples

Show / Hide Samples